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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggataattttttctccagttctcaatctttgtctcatatttatattctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT

Basic information

species Vitis vinifera
transcript Vv01s0026g00920.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g22440.1 (Oryza sativa), 3'ss of exon 1
-ggataattttttctccagttctcaatctttgt--ctcatatttatattctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT
  |  || |   | || | || |||   || |    | | ||   | || || ||||||    |||   |     ||| | |  |||||||| |  |   ||||| |||  |||| | |||||||| || |||||||| ||||| ||||||||||||||| |  | || ||||| ||||| ||| |||||||||| || |  |
atgcaaagtgcatatcaaattatcagcattggcagttaagatgattgttgttattatgagtttgttcttaac---atattttattttttgttgttatatgcagACTGCTTCAGCTAAGAGTTGGACATGCATGGATCTCTATGTGTTTGCAACACCATATAGGATAACATGGGATTACTATTTTGCTGCTCGAGAACACACTT

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G031824_T01 (Zea mays), 3'ss of exon 1
ggataattttttctccagttctcaatctttgtct-catatttatattctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT
||| |      | | |     |   || || | |  ||  | |   ||  ||  |  |    || |     ||| | |    ||||  ||   ||   ||||| |||  |||||| |||||| | || |||||||| || |||||||||||||||||| |  | || |||||||| || ||| ||||||| ||||| |  |
ggacaggaccatttactaagattggtcgttttatatatgatcagggtcacttattattttctttacgtaagtga-agttgttttttcctttgtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTT

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G04400.1 (Glycine max), 3'ss of exon 1
--------ggataattttttctccagttctcaatctttgtctcatatttatattctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT
        ||||  |||  |    | || | | | | ||||   ||||| |   |  ||| || | |   || |   | |  ||| | |   |||  || || |  ||||||  |  || |||||||||||||| |||||||| ||||||||||||||||| ||| |  |||| ||||||||||| || ||||| ||||| ||||  |
ttttggttggattgtttgatgagaaatt-taagtatctgtcct-tatttgt---ccctttctgctccctctttataat-gtgaattttaacattggccttttac--agACAGAAGCTGCACACAGTTGGACCTGCATGGATCTGTATGTTTTTGCAACACCTTATAGGATTACATGGGACTACTATTTCTCTGCGCGAGAACATACTT

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G03160.1 (Glycine max), 3'ss of exon 1
--------ggataattttttctccagttctcaatctttgtctcatatttatattctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT
        ||||   ||  |    | || | | | | |||||    ||  |  ||  ||| || | |   || |   | |  |||   | | |||  || || |  ||||||  |  ||||||||||||||||| |||||||| ||||| |||||||| || ||| |  |||| ||||| ||||| || ||||| ||||| ||||  |
ttttggttggattgcttgatgagaaatttt-agtatctgtct----ttggttgtccctttctgctccccctttataat-gtgaattataatattggccttttac--agACAGAAGCTGCTCACAGTTGGACCTGCATGGATCTGTATGTATTTGCAACGCCTTATAGGATTACATGGGATTACTATTTCTCTGCGCGAGAACATACTT

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G17350.1 (Glycine max), 3'ss of exon 1
-----ggataattttttctccagttctcaatctttgtctcatatttat--attctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT
      |  |||||||  |   ||| ||  | | || || || ||  |  ||  | |  || ||||  || |   | ||| |     ||  ||||||| ||   |||||||  |  || || || |||||||| |||||| | ||||||||||||||||| ||  |  |||| |||||||||||||| ||| | ||||| ||||   
ttaattggaaatttttaatgt-gttttctgt-tatgccttatgttgcttgatgatatggattatacgtttcctttgctgaaa----tataattgttcttttttacaGACAGAGGCTGCACATAGCTGGACCTGCATGGATTTGTATGTTTTTGCAACACCCTACAGGATTACTTGGGACTACTACTTCTCTTCACGAGAACATACC-

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110708417|gb|EE085938.1|EE085938
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|161719352|gb|FC064843.1|FC064843
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|110687415|gb|EE064806.1|EE064806
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|18458236|gb|BM436514.1|BM436514
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|71863453|gb|DT012508.1|DT012508
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|351025013|gb|FQ433430.1|FQ433430
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|351030083|gb|FQ430825.1|FQ430825
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|110412793|gb|EC978554.1|EC978554
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACA
EST: gi|161709013|gb|FC060945.1|FC060945
EST:     AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACG                         ACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTAT
genomic: AGTTTACCAGCGGCGACAGAGGTCTGGGTGGTGGCGTTCTTTATCTCACGgtttgagctc ... tcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT
                      ggttgat  putative branch site (score: 5)
                               tctcatttttgttctc  putative PPT
                           ataatctcattttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggataattttttctccagttctcaatctttgtctcatatttatattctttttatgatacagtttcaaggttgataatctcatttttgttctcttcctcagACAGCTGAAGCTCACAGTTGGACCTGTATGGATCTATATGTTTTTGCAACACCATATCGTGTTACGTGGGACTACTACTTTTCTGCTCGAGAGCATAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - ttctcca
- - - - - - - - - - - - - - -tgtctca